GraphicsPanel (computational omics utilities 4.5.7 API)

java.lang.Object
- java.awt.Component
- - java.awt.Container
  - - javax.swing.JComponent
    - - javax.swing.JPanel
      - com.compomics.util.gui.spectrum.GraphicsPanel

All Implemented Interfaces:

ImageObserver, MenuContainer, Serializable, Accessible

Direct Known Subclasses:

ChromatogramPanel, IsotopicDistributionPanel, SpectrumPanel
```
public abstract class GraphicsPanel
extends JPanel
```
This class presents a JPanel that will hold and display a mass spectrum or a chromatogram.

Author:

Lennart Martens, Harald Barsnes

See Also:

Serialized Form

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`static class`	`GraphicsPanel.DrawingStyle` An enumerator of the possible GraphicsPanel types.
`protected static class`	`GraphicsPanel.GraphicsPanelType` An enumerator of the possible GraphicsPanel types.

Nested classes/interfaces inherited from class javax.swing.JPanel
JPanel.AccessibleJPanel

Nested classes/interfaces inherited from class javax.swing.JComponent
JComponent.AccessibleJComponent

Nested classes/interfaces inherited from class java.awt.Container
Container.AccessibleAWTContainer

Nested classes/interfaces inherited from class java.awt.Component
Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy

Field Summary

Fields
Modifier and Type	Field and Description
`protected float`	`alphaLevel` The opacity of the spectra.
`int`	`ANNOTATED_STATUS` This status indicates that annotation (if present) will be displayed, while limiting the user to zooming in/out.
`protected boolean`	`annotateHighestPeak` If more than one peak is within the accuracy range of an annotation setting this to true will always select the most intense of possible peaks.
`protected GraphicsPanel.GraphicsPanelType`	`currentGraphicsPanelType` Sets the current GraphicsPanel type, default to centroid spectrum.
`protected int`	`currentPadding` The current padding (distance between the axes and the border of the panel).
`protected int`	`dataSetCounter` The number of datasets currently displayed in the panel.
`protected int`	`dataSetCounterMirroredSpectra` The number of mirrored datasets currently displayed in the panel.
`protected double`	`deltaMassWindow` The size of the window to use when searching for matches in the known masses list when the user hovers over a second data point after clicking a previous data point.
`protected Vector`	`iAnnotations` The Vector that holds a set of Annotation instances.
`protected Vector`	`iAnnotationsMirroredSpectra` The Vector that holds a set of Annotation instances for the mirrored spectra.
`protected double`	`iAnnotationYAxisThreshold` The percent non-inclusive, minimal y-axis value (compared to the highest point in the spectrum) a point should have before being eligible for annotation.
`protected ArrayList<Color>`	`iAreaUnderCurveColor` Colors in which the chromatogram polyline is rendered.
`protected ArrayList<Color>`	`iAreaUnderCurveColorMirroredSpectra` Colors in which the chromatogram polyline is rendered for the mirrored spectra.
`protected boolean`	`iClicked` Boolean that indicates whether a point has been marked by clicking.
`protected int`	`iClickedDataSetIndex` Int that indicates which dataset contains the clicked point.
`protected int`	`iClickedDataSetIndexMirrored` Int that indicates which dataset contains the clicked point in the mirrored spectra.
`protected int`	`iClickedIndex` Int that indicates which point was clicked.
`protected int`	`iClickedIndexMirrored` Int that indicates which point was clicked in the mirrored spectra.
`protected Vector`	`iClickedList` The Vector that holds all points clicked up to now.
`protected Vector`	`iClickedListDatasetIndices` The Vector that holds the dataset indices of all points clicked up to now.
`protected Vector`	`iClickedListDatasetIndicesMirrored` The Vector that holds the dataset indices of all points clicked up to now in the mirrored spectra.
`protected Vector`	`iClickedListMirrored` The Vector that holds all points clicked up to now in the mirrored spectra.
`protected boolean`	`iClickedMirrored` Boolean that indicates whether a point has been marked by clicking in the mirrored spectra.
`protected GraphicsPanel.DrawingStyle`	`iCurrentDrawStyle` This variable holds the current drawing style.
`protected ArrayList<Color>`	`iDataPointAndLineColor` Colors in which the data points and peaks are rendered.
`protected ArrayList<Color>`	`iDataPointAndLineColorMirroredSpectra` Colors in which the data points and peaks are rendered for the mirrored spectra.
`protected int`	`iDotRadius` This variable holds the dot radius; only used when drawing style is DOTS style.
`protected boolean`	`iDragged` This boolean is set to 'true' when dragging is performed.
`protected int`	`iDragXLoc` The current dragging location.
`protected int`	`iEndXLoc` When the mouse is dragged, this represents the X-coordinate of the ending location.
`protected String`	`iFilename` The spectrum or chromatogram filename.
`protected Color`	`iFilenameColor` This is the color the filename should be presented in.
`protected String`	`iFilenameMirrorredSpectrum` The spectrum or chromatogram filename for the mirrored spectrum or chromatogram.
`protected boolean`	`iHighLight` Boolean that will be 'true' when a point needs highlighting.
`protected int`	`iHighLightDatasetIndex` Index of the dataset containing the point that needs to be highlighted.
`protected int`	`iHighLightDatasetIndexMirrored` Index of the dataset containing the point that needs to be highlighted in the mirrored spectra.
`protected int`	`iHighLightIndex` Index of the point that needs to be highlighted.
`protected int`	`iHighLightIndexMirrored` Index of the point that needs to be highlighted in the mirrored spectra.
`protected boolean`	`iHighLightMirrored` Boolean that will be 'true' when a point needs highlighting in the mirrored spectra.
`protected static HashMap<Double,String>`	`iKnownMassDeltas` This HashMap instance holds all the known mass deltas (if any).
`protected int`	`iMinDrag` Minimal dragging distance in pixels.
`protected int`	`iMSLevel` The ms level of the current spectrum.
`int`	`INTERACTIVE_STATUS` This status indicates that no annotation will be displayed, but the user will have a fully functional interface (point clicking, selecting, sequencing etc.)
`protected int`	`iPointDetectionTolerance` The deviation (both left and right) allowed for point highlighting detection.
`protected Integer`	`iPointSize` Size for the point on a polygon.
`protected String`	`iPrecursorCharge` This String holds the charge for the precursor.
`protected String`	`iPrecursorChargeMirorredSpectrum` This String holds the charge for the precursor for the mirrored spectrum.
`protected double`	`iPrecursorMZ` This variable holds the precursor M/Z.
`protected double`	`iPrecursorMZMirroredSpectrum` This variable holds the precursor M/Z for the mirrored spectrum.
`protected ArrayList`	`iSpecPanelListeners` The list of SpectrumPanelListeners.
`protected int`	`iStartXLoc` When the mouse is dragged, this represents the X-coordinate of the starting location.
`protected int`	`iStartYLoc` When the mouse is dragged, this represents the Y-coordinate of the starting location.
`protected Vector`	`iStoredSequence` The Vector that holds a set of stored points from a previously established list.
`protected Vector`	`iStoredSequenceDatasetIndices` The Vector that holds the dataset indices of stored points from a previously established list.
`protected Vector`	`iStoredSequenceDatasetIndicesMirrored` The Vector that holds the dataset indices of stored points from a previously established list in the mirrored spectra.
`protected Vector`	`iStoredSequenceMirrored` The Vector that holds a set of stored points from a previously established list in the mirrored spectra.
`protected int`	`iTopPadding` Effective distance from the panel top border to 5 pixels above the top of the highest point (or y-tick mark).
`protected ArrayList<double[]>`	`iXAxisData` All the x-axis data points.
`protected ArrayList<int[]>`	`iXAxisDataInPixels` This array will hold the x-coordinates in pixels for all the x-axis values.
`protected ArrayList<int[]>`	`iXAxisDataInPixelsMirroredSpectrum` This array will hold the x-coordinates in pixels for all the x-axis values of the mirrored spectrum.
`protected ArrayList<double[]>`	`iXAxisDataMirroredSpectrum` All the x-axis data points for the mirrored spectrum.
`protected String`	`iXAxisLabel` The label (and unit between brackets, if available) for the x-axis.
`protected double`	`iXAxisMax` The maximum x-axis value to display.
`protected double`	`iXAxisMin` The minimum x-axis value to display.
`protected boolean`	`iXAxisStartAtZero` This boolean is set to 'true' if the x-axis should start at zero.
`protected int`	`iXPadding` Effective distance from the x-axis to the panel border.
`protected double`	`iXScaleUnit` Scale unit for the X axis.
`protected int`	`iXUnit` Graphical unit for the X axis.
`protected ArrayList<double[]>`	`iYAxisData` All the y-axis values.
`protected ArrayList<int[]>`	`iYAxisDataInPixels` This array will hold the y-coordinates in pixels for all the y-axis values.
`protected ArrayList<int[]>`	`iYAxisDataInPixelsMirroredSpectrum` This array will hold the y-coordinates in pixels for all the y-axis values of the mirrored spectrum.
`protected ArrayList<double[]>`	`iYAxisDataMirroredSpectrum` All the y-axis values for the mirrored spectra.
`protected String`	`iYAxisLabel` The label (and unit between brackets, if available) for the y-axis.
`protected double`	`iYAxisMax` The maximum y-axis value to display.
`protected double`	`iYAxisMin` The minimum y-axis value to display.
`protected double`	`iYScaleUnit` Scale unit for the Y axis.
`protected int`	`iYUnit` Graphical unit for the Y axis.
`protected int`	`maxPadding` The maximum padding (distance between the axes and the border of the panel).
`protected boolean`	`miniature` If set to true, the y-axis is removed, the y- and x-axis tags are removed, and any annotations are hidden.
`protected int`	`padding` The padding (distance between the axes and the border of the panel).
`protected boolean`	`showAllPeaks` If false, only the annotated peaks will be shown.
`protected boolean`	`showFileName` The boolean is set to 'true' if the file name is to be shown in the panel.
`protected boolean`	`showPrecursorDetails` The boolean is set to 'true' if the precursor details is to be shown in the panel.
`protected boolean`	`showResolution` The boolean is set to 'true' if the resolution is to be shown in the panel.
`protected double`	`xAxisZoomRangeLowerValue` The lower range for the current zoom range.
`protected double`	`xAxisZoomRangeUpperValue` The upper range for the current zoom range.
`protected int`	`xTagCount` The number of X-axis tags.
`protected boolean`	`yAxisZoomExcludesBackgroundPeaks` If true, the automatic y-axis zoom excludes the background peaks.
`protected boolean`	`yDataIsPositive` If set to true, all y data is assumed to be positive.
`protected int`	`yTagCount` The number of Y-axis tags.

Fields inherited from class javax.swing.JComponent
listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW

Fields inherited from class java.awt.Component
accessibleContext, BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

Constructors
Constructor and Description

GraphicsPanel()

Constructors
Constructor and Description
`GraphicsPanel()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected void`	`addListeners()` This method adds the event listeners to the panel.
`void`	`addReferenceAreaXAxis(ReferenceArea referenceArea)` Add a x-axis reference area.
`void`	`addReferenceAreaYAxis(ReferenceArea referenceArea)` Add a y-axis reference area.
`void`	`addSpectrumPanelListener(SpectrumPanelListener aListener)` This method registers the specified SpectrumPanelListener with this instance and notifies it of all future events.
`protected void`	`annotate(SpectrumAnnotation aSA, Graphics g, HashMap<String,Integer> aAlreadyAnnotated, boolean mirrored)` This method attempts to find the specified SpectrumAnnotation in the current peak list and if so, annotates it correspondingly on the screen.
`protected void`	`annotatePeaks(Graphics g, Vector annotations, boolean mirrored)` Annotate the annotated peaks.
`protected int[]`	`drawAxes(Graphics g, double aXMin, double aXMax, int aXScale, double aYMin, double aYMax)` This method draws the axes and their labels on the specified Graphics object, taking into account the padding.
`protected void`	`drawDaisyChain(Graphics g, Vector clickedList, Vector clickedListDatasetIndices, int clickedIndex, int clickedDataSetIndex, Vector storedSequence, Vector storedSequenceDatasetIndices, boolean mirrored)` Draw daisy chains.
`protected void`	`drawFilledPolygon(Graphics g)` This method draws filled polygons for all of the peaks for all datasets in the current x-axis range on the panel.
`protected void`	`drawMeasurementLine(int aFirstIndex, int aFirstDatasetIndex, int aSecondIndex, int aSecondDatasetIndex, Graphics g, Color aColor, int aExtraPadding, boolean mirrored)` This method draws a line, measuring the distance between two points in real mass units.
`protected void`	`drawMirroredPeaks(Graphics g)` This method draws all of the peaks for all datasets in the current x-axis range on the panel.
`protected void`	`drawPeaks(Graphics g)` This method draws all of the peaks for all datasets in the current x-axis range on the panel.
`protected void`	`drawXAxisReferenceAreas(Graphics g, boolean drawOnTop)` Draws the x-axis reference areas if any.
`protected void`	`drawXTags(Graphics g, int aMin, int aMax, int aXScale, int aXAxisWidth, int aPadding)` This method draws tags on the X axis.
`protected void`	`drawYAxisReferenceAreas(Graphics g, boolean drawOnTop)` Draws the y-axis reference areas if any.
`protected void`	`drawYTags(Graphics g, int aMin, int aMax, int aYAxisHeight, int aPadding)` This method draws tags on the Y axis.
`protected void`	`dropDottedLine(int aPeakIndex, int aDatasetIndex, int aTotalHeight, Graphics g, boolean mirrored)` This method drops a dotted line from the specified total height to the top of the indicated point.
`protected String`	`findDeltaMassMatches(double aDelta, double aWindow)` This method attempts to find a list of known mass deltas, corresponding with the specified x value in the given window.
`HashMap<String,ReferenceArea>`	`getAllReferenceAreasXAxis()` Returns all the x-axis references areas as a hashmap, with the labels as the keys.
`HashMap<String,ReferenceArea>`	`getAllReferenceAreasYAxis()` Returns all the y-axis references areas as a hashmap, with the labels as the keys.
`float`	`getAlphaLevel()` Returns the alpha level.
`ArrayList<Color>`	`getAreaUnderCurveColors()` Returns the list of colors used for the datasets.
`float`	`getBackgroundPeakWidth()` Returns the current width of the background peaks.
`double`	`getDeltaMassWindow()` Get the size of the window to use when searching for matches in the known masses list when the user hovers over a second data point after clicking a previous data point.
`double`	`getiXAxisMax()` Returns the maximum value of the x-axis.
`double`	`getiXAxisMin()` Returns the minimum value of the x-axis.
`double`	`getiYAxisMax()` Returns the maximum value of the y-axis.
`double`	`getiYAxisMin()` Returns the minimum value of the y-axis.
`static HashMap<Double,String>`	`getKnownMassDeltas()` Get all the known mass deltas (if any).
`int`	`getMaxPadding()` Returns the max padding (distance between the axes and the border of the panel).
`double`	`getMaxXAxisValue()` This method reports on the largest x-axis value in the point collection across all datasets.
`double`	`getMinXAxisValue()` This method reports on the smallest x-axis value in the point collection across all datasets.
`Color`	`getPeakWaterMarkColor()` Get the peak water mark color.
`float`	`getPeakWidth()` Returns the current width of the peaks.
`ArrayList<double[]>`	`getXAxisData()` Returns the x-axis data.
`double`	`getXAxisZoomRangeLowerValue()` Returns the lower range for the current zoom range.
`double`	`getXAxisZoomRangeUpperValue()` Returns the upper range for the current zoom range.
`ArrayList<double[]>`	`getYAxisData()` Returns the y-axis data.
`protected void`	`highLight(int aIndex, int dataSetIndex, Graphics g, Color aColor, String aComment, int aPixelsSpacer, boolean aShowArrow, int aAnnotationCounter, boolean mirrored)` This method will highlight the specified point in the specified color by drawing a floating triangle + x-value above it.
`protected void`	`highlightClicked(int aIndex, int dataSetIndex, Graphics g, boolean mirrored)` This method will draw a highlighting triangle + x-value on top of the clicked marked point.
`protected void`	`highLightPeak(int aIndex, int dataSetIndex, Graphics g, boolean mirrored)` This method will draw a highlighting triangle + x-value on top of the marked point.
`boolean`	`isAnnotateHighestPeak()` Returns true if the most intense of possible peaks to annotate is to be selected, false if the most accurate is to be selected.
`boolean`	`isMiniature()` Returns true if the graphics panel is to be drawn in a miniature form.
`boolean`	`isSubscriptAnnotationNumbers()` Returns true if the numbers in the peak annotations are to be subscripted.
`void`	`paint(Graphics g)` Invoked by Swing to draw components.
`protected void`	`processMirroredXAndYData(double[] aXAxisData, double[] aYAxisData, Color dataPointAndLineColor, Color areaUnderCurveColor)` This method reads the x and y values from the specified arrays and stores these internally for drawing.
`protected void`	`processXAndYData(double[] aXAxisData, double[] aYAxisData, Color dataPointAndLineColor, Color areaUnderCurveColor)` This method reads the x and y values from the specified arrays and stores these internally for drawing.
`void`	`removeAllReferenceAreasXAxis()` Removes all the x-axis reference areas.
`void`	`removeAllReferenceAreasYAxis()` Removes all the y-axis reference areas.
`void`	`removeReferenceAreaXAxis(String identifier)` Removes the x-axis reference area with the given identifier.
`void`	`removeReferenceAreaYAxis(String identifier)` Removes the y-axis reference area with the given identifier.
`void`	`rescale(double aMinXAxisValue, double aMaxXAxisValue)` This method rescales the x-axis while notifying the observers.
`void`	`rescale(double aMinXAxisValue, double aMaxXAxisValue, boolean aNotifyListeners)` This method rescales the x-axis, allowing the caller to specify whether the observers need be notified.
`void`	`setAlphaLevel(float alphaLevel)` Sets the alpha level
`void`	`setAnnotateHighestPeak(boolean annotateHighestPeak)` Set if the most intense of possible peaks to annotate is to be selected, false if the most accurate is to be selected.
`void`	`setAnnotations(List<SpectrumAnnotation> aAnnotations)` This method sets all the annotations on this instance.
`void`	`setAnnotations(List<SpectrumAnnotation> aAnnotations, boolean annotateHighestPeak)` This method sets all the annotations on this instance.
`void`	`setAnnotationsMirrored(List<SpectrumAnnotation> aAnnotations)` This method sets all the annotations for the mirrored spectra.
`void`	`setAnnotationsMirrored(List<SpectrumAnnotation> aAnnotations, boolean annotateHighestPeak)` This method sets all the annotations for the mirrored spectra.
`void`	`setAnnotationYAxisThreshold(double aThreshold)` This method allows the caller to set the minimal non-inclusive y-axis value threshold in percent (compared to the highest point in the spectrum or chromatogram) a point must pass before being eligible for annotation.
`void`	`setAreaUnderCurveColor(Color aColor, int index)` Sets the color of the area under the curve for profile chromatograms and spectra for the dataset with the given dataset index.
`void`	`setBackgroundPeakWidth(float backgroundPeakWidth)` Set the backgroundPeakWidth peak width.
`void`	`setDataPointAndLineColor(Color aColor, int index)` Sets the color of data points and line for the dataset with the given dataset index.
`void`	`setDeltaMassWindow(double deltaMassWindow)` Set the size of the window to use when searching for matches in the known masses list when the user hovers over a second data point after clicking a previous data point.
`void`	`setFilenameColor(Color aFilenameColor)` This method sets the display color for the filename on the panel.
`void`	`setiXAxisMax(double aXAxisMax)` Sets the maximum value for the x-axis.
`void`	`setiXAxisMin(double aXAxisMin)` Sets the minimum value for the x-axis.
`void`	`setiYAxisMax(double aYAxisMax)` Sets the maximum value for the y-axis.
`void`	`setiYAxisMin(double aYAxisMin)` Sets the minimum value for the y-axis.
`static void`	`setKnownMassDeltas(HashMap<Double,String> aiKnownMassDeltas)` Set all the known mass deltas (if any).
`void`	`setMaxPadding(int aMaxPadding)` Set the max padding (distance between the axes and the border of the panel).
`void`	`setMiniature(boolean miniature)` Set if the graphics panel is to be drawn in a miniature form.
`void`	`setPeakWaterMarkColor(Color peakWaterMarkColor)` Set the peak water mark color.
`void`	`setPeakWidth(float peakWidth)` Set the peak width.
`void`	`setScientificXAxis(boolean scientificXAxis)` Set if the x-axis tags are to be drawn using scientific annotation.
`void`	`setScientificXAxis(String pattern)` Set if the x-axis tags are to be drawn using scientific annotation.
`void`	`setScientificYAxis(boolean scientificYAxis)` Set if the y-axis tags are to be drawn using scientific annotation.
`void`	`setScientificYAxis(String pattern)` Set if the y-axis tags are to be drawn using scientific annotation.
`void`	`setShowPrecursorDetails(boolean showPrecursorDetails)` Set whether the precursor details are to be shown.
`void`	`setShowResolution(boolean showResolution)` Set whether the resolution is to be shown.
`void`	`setSubscriptAnnotationNumbers(boolean subscriptAnnotationNumbers)` Set if the numbers in the peak annotations are to be subscripted.
`void`	`setUseMassDeltaCombinations(boolean useMassDeltaCombinations)` If true, pairs of delta mass annotations are used when doing de novo sequencing.
`void`	`setXAxisStartAtZero(boolean aXAxisStartAtZero)` This method sets the start value of the x-axis to zero.
`void`	`setYAxisZoomExcludesBackgroundPeaks(boolean yAxisZoomExcludesBackgroundPeaks)` Set if the automatic y-axis zoom only considers the annotated peaks.
`void`	`setYDataIsPositive(boolean yDataIsPositive)` Set to true of all y data values can be assumed to be positive.
`boolean`	`showPrecursorDetails()` Returns true of the precursor details are to be shown.
`boolean`	`showResolution()` Returns true if the resolution is to be shown.
`boolean`	`useMassDeltaCombinations()` If true, pairs of delta mass annotations are used when doing de novo sequencing.
`boolean`	`yAxisZoomOnlyExcludesBackgroundPeaks()` Returns true if the automatic y-axis zoom excludes background peaks.
`boolean`	`yDataIsPositive()` Returns true of all the y-data is to be assumed as positive.

Methods inherited from class javax.swing.JPanel
getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI

Methods inherited from class javax.swing.JComponent
addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update

Methods inherited from class java.awt.Container
add, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusDownCycle, validate, validateTree

Methods inherited from class java.awt.Component
action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - miniature
```
protected boolean miniature
```
    If set to true, the y-axis is removed, the y- and x-axis tags are removed, and any annotations are hidden. All to make the graphics panel look better in a smaller version, e.g., when put into a table cell. When turning miniature mode one it is also recommended to reduce the max padding. Note that miniature and reduced max padding is set automatically by the GraphicsPanelTableCellRenderer.
  - yDataIsPositive
```
protected boolean yDataIsPositive
```
    If set to true, all y data is assumed to be positive. This adds a white polygon under the y-axis hiding any polygon data lines that crosses (slightly) below the y-axis.
  - alphaLevel
```
protected float alphaLevel
```
    The opacity of the spectra. 0 means completely see-through, 1 means opaque.
  - dataSetCounter
```
protected int dataSetCounter
```
    The number of datasets currently displayed in the panel.
  - dataSetCounterMirroredSpectra
```
protected int dataSetCounterMirroredSpectra
```
    The number of mirrored datasets currently displayed in the panel.
  - INTERACTIVE_STATUS
```
public final int INTERACTIVE_STATUS
```
    This status indicates that no annotation will be displayed, but the user will have a fully functional interface (point clicking, selecting, sequencing etc.)
    
    See Also:
    
    Constant Field Values
  - ANNOTATED_STATUS
```
public final int ANNOTATED_STATUS
```
    This status indicates that annotation (if present) will be displayed, while limiting the user to zooming in/out.
    
    See Also:
    
    Constant Field Values
  - iKnownMassDeltas
```
protected static HashMap<Double,String> iKnownMassDeltas
```
    This HashMap instance holds all the known mass deltas (if any). The keys are the Doubles with the massdelta, the values are the descriptions.
  - deltaMassWindow
```
protected double deltaMassWindow
```
    The size of the window to use when searching for matches in the known masses list when the user hovers over a second data point after clicking a previous data point.
  - iXAxisLabel
```
protected String iXAxisLabel
```
    The label (and unit between brackets, if available) for the x-axis. Defaults to "m/z".
  - iYAxisLabel
```
protected String iYAxisLabel
```
    The label (and unit between brackets, if available) for the y-axis. Defaults to "Int".
  - iFilenameColor
```
protected Color iFilenameColor
```
    This is the color the filename should be presented in.
  - iDataPointAndLineColor
```
protected ArrayList<Color> iDataPointAndLineColor
```
    Colors in which the data points and peaks are rendered. Indexed by dataset.
  - iDataPointAndLineColorMirroredSpectra
```
protected ArrayList<Color> iDataPointAndLineColorMirroredSpectra
```
    Colors in which the data points and peaks are rendered for the mirrored spectra. Indexed by dataset.
  - iAreaUnderCurveColor
```
protected ArrayList<Color> iAreaUnderCurveColor
```
    Colors in which the chromatogram polyline is rendered. Indexed by dataset.
  - iAreaUnderCurveColorMirroredSpectra
```
protected ArrayList<Color> iAreaUnderCurveColorMirroredSpectra
```
    Colors in which the chromatogram polyline is rendered for the mirrored spectra. Indexed by dataset.
  - iPointSize
```
protected Integer iPointSize
```
    Size for the point on a polygon.
  - iFilename
```
protected String iFilename
```
    The spectrum or chromatogram filename.
  - iFilenameMirrorredSpectrum
```
protected String iFilenameMirrorredSpectrum
```
    The spectrum or chromatogram filename for the mirrored spectrum or chromatogram.
  - iSpecPanelListeners
```
protected ArrayList iSpecPanelListeners
```
    The list of SpectrumPanelListeners.
  - iPointDetectionTolerance
```
protected int iPointDetectionTolerance
```
    The deviation (both left and right) allowed for point highlighting detection.
  - iStartXLoc
```
protected int iStartXLoc
```
    When the mouse is dragged, this represents the X-coordinate of the starting location.
  - iStartYLoc
```
protected int iStartYLoc
```
    When the mouse is dragged, this represents the Y-coordinate of the starting location.
  - iEndXLoc
```
protected int iEndXLoc
```
    When the mouse is dragged, this represents the X-coordinate of the ending location.
  - xAxisZoomRangeLowerValue
```
protected double xAxisZoomRangeLowerValue
```
    The lower range for the current zoom range.
  - xAxisZoomRangeUpperValue
```
protected double xAxisZoomRangeUpperValue
```
    The upper range for the current zoom range.
  - iDragXLoc
```
protected int iDragXLoc
```
    The current dragging location.
  - iXScaleUnit
```
protected double iXScaleUnit
```
    Scale unit for the X axis.
  - iYScaleUnit
```
protected double iYScaleUnit
```
    Scale unit for the Y axis.
  - iXUnit
```
protected int iXUnit
```
    Graphical unit for the X axis.
  - iYUnit
```
protected int iYUnit
```
    Graphical unit for the Y axis.
  - iXPadding
```
protected int iXPadding
```
    Effective distance from the x-axis to the panel border.
  - iTopPadding
```
protected int iTopPadding
```
    Effective distance from the panel top border to 5 pixels above the top of the highest point (or y-tick mark).
  - iXAxisStartAtZero
```
protected boolean iXAxisStartAtZero
```
    This boolean is set to 'true' if the x-axis should start at zero.
  - iDragged
```
protected boolean iDragged
```
    This boolean is set to 'true' when dragging is performed.
  - xTagCount
```
protected int xTagCount
```
    The number of X-axis tags.
  - yTagCount
```
protected int yTagCount
```
    The number of Y-axis tags.
  - padding
```
protected int padding
```
    The padding (distance between the axes and the border of the panel).
  - currentPadding
```
protected int currentPadding
```
    The current padding (distance between the axes and the border of the panel).
  - maxPadding
```
protected int maxPadding
```
    The maximum padding (distance between the axes and the border of the panel). Increase if font size on the y-axis becomes too small.
  - showFileName
```
protected boolean showFileName
```
    The boolean is set to 'true' if the file name is to be shown in the panel.
  - showPrecursorDetails
```
protected boolean showPrecursorDetails
```
    The boolean is set to 'true' if the precursor details is to be shown in the panel.
  - showResolution
```
protected boolean showResolution
```
    The boolean is set to 'true' if the resolution is to be shown in the panel.
  - iXAxisData
```
protected ArrayList<double[]> iXAxisData
```
    All the x-axis data points. Indexed by dataset (one double[] per dataset). First dataset is the first double[], second dataset is the second double[] etc.Should at all times be sorted from high to low.
  - iXAxisDataMirroredSpectrum
```
protected ArrayList<double[]> iXAxisDataMirroredSpectrum
```
    All the x-axis data points for the mirrored spectrum. Indexed by dataset (one double[] per dataset). First dataset is the first double[], second dataset is the second double[] etc.Should at all times be sorted from high to low.
  - iXAxisMin
```
protected double iXAxisMin
```
    The minimum x-axis value to display.
  - iXAxisMax
```
protected double iXAxisMax
```
    The maximum x-axis value to display.
  - iYAxisMin
```
protected double iYAxisMin
```
    The minimum y-axis value to display.
  - iYAxisMax
```
protected double iYAxisMax
```
    The maximum y-axis value to display.
  - iAnnotationYAxisThreshold
```
protected double iAnnotationYAxisThreshold
```
    The percent non-inclusive, minimal y-axis value (compared to the highest point in the spectrum) a point should have before being eligible for annotation. Default is '0.0'.
  - iYAxisData
```
protected ArrayList<double[]> iYAxisData
```
    All the y-axis values. Indexed by dataset (one double[] per dataset). First dataset is the first double[], second dataset is the second double[] etc. Y-axis values are related to the x-axis values by the table index. So the first y-axis value of the first dataset is the value for the first x-axis value in the first dataset etc.
  - iYAxisDataMirroredSpectrum
```
protected ArrayList<double[]> iYAxisDataMirroredSpectrum
```
    All the y-axis values for the mirrored spectra. Indexed by dataset (one double[] per dataset). First dataset is the first double[], second dataset is the second double[] etc. Y-axis values are related to the x-axis values by the table index. So the first y-axis value of the first dataset is the value for the first x-axis value in the first dataset etc.
  - iPrecursorMZ
```
protected double iPrecursorMZ
```
    This variable holds the precursor M/Z.
  - iPrecursorMZMirroredSpectrum
```
protected double iPrecursorMZMirroredSpectrum
```
    This variable holds the precursor M/Z for the mirrored spectrum.
  - iPrecursorCharge
```
protected String iPrecursorCharge
```
    This String holds the charge for the precursor.
  - iPrecursorChargeMirorredSpectrum
```
protected String iPrecursorChargeMirorredSpectrum
```
    This String holds the charge for the precursor for the mirrored spectrum.
  - iXAxisDataInPixels
```
protected ArrayList<int[]> iXAxisDataInPixels
```
    This array will hold the x-coordinates in pixels for all the x-axis values. Link is through index. Again indexed by dataset (one double[] per dataset).
  - iYAxisDataInPixels
```
protected ArrayList<int[]> iYAxisDataInPixels
```
    This array will hold the y-coordinates in pixels for all the y-axis values. Link is through index. Again indexed by dataset (one double[] per dataset).
  - iXAxisDataInPixelsMirroredSpectrum
```
protected ArrayList<int[]> iXAxisDataInPixelsMirroredSpectrum
```
    This array will hold the x-coordinates in pixels for all the x-axis values of the mirrored spectrum. Link is through index. Again indexed by dataset (one double[] per dataset).
  - iYAxisDataInPixelsMirroredSpectrum
```
protected ArrayList<int[]> iYAxisDataInPixelsMirroredSpectrum
```
    This array will hold the y-coordinates in pixels for all the y-axis values of the mirrored spectrum. Link is through index. Again indexed by dataset (one double[] per dataset).
  - iHighLight
```
protected boolean iHighLight
```
    Boolean that will be 'true' when a point needs highlighting.
  - iHighLightMirrored
```
protected boolean iHighLightMirrored
```
    Boolean that will be 'true' when a point needs highlighting in the mirrored spectra.
  - iHighLightIndex
```
protected int iHighLightIndex
```
    Index of the point that needs to be highlighted.
  - iHighLightIndexMirrored
```
protected int iHighLightIndexMirrored
```
    Index of the point that needs to be highlighted in the mirrored spectra.
  - iHighLightDatasetIndex
```
protected int iHighLightDatasetIndex
```
    Index of the dataset containing the point that needs to be highlighted.
  - iHighLightDatasetIndexMirrored
```
protected int iHighLightDatasetIndexMirrored
```
    Index of the dataset containing the point that needs to be highlighted in the mirrored spectra.
  - iClicked
```
protected boolean iClicked
```
    Boolean that indicates whether a point has been marked by clicking.
  - iClickedMirrored
```
protected boolean iClickedMirrored
```
    Boolean that indicates whether a point has been marked by clicking in the mirrored spectra.
  - iClickedIndex
```
protected int iClickedIndex
```
    Int that indicates which point was clicked.
  - iClickedIndexMirrored
```
protected int iClickedIndexMirrored
```
    Int that indicates which point was clicked in the mirrored spectra.
  - iClickedDataSetIndex
```
protected int iClickedDataSetIndex
```
    Int that indicates which dataset contains the clicked point.
  - iClickedDataSetIndexMirrored
```
protected int iClickedDataSetIndexMirrored
```
    Int that indicates which dataset contains the clicked point in the mirrored spectra.
  - iClickedList
```
protected Vector iClickedList
```
    The Vector that holds all points clicked up to now.
  - iClickedListMirrored
```
protected Vector iClickedListMirrored
```
    The Vector that holds all points clicked up to now in the mirrored spectra.
  - iClickedListDatasetIndices
```
protected Vector iClickedListDatasetIndices
```
    The Vector that holds the dataset indices of all points clicked up to now.
  - iClickedListDatasetIndicesMirrored
```
protected Vector iClickedListDatasetIndicesMirrored
```
    The Vector that holds the dataset indices of all points clicked up to now in the mirrored spectra.
  - iStoredSequence
```
protected Vector iStoredSequence
```
    The Vector that holds a set of stored points from a previously established list.
  - iStoredSequenceMirrored
```
protected Vector iStoredSequenceMirrored
```
    The Vector that holds a set of stored points from a previously established list in the mirrored spectra.
  - iStoredSequenceDatasetIndices
```
protected Vector iStoredSequenceDatasetIndices
```
    The Vector that holds the dataset indices of stored points from a previously established list.
  - iStoredSequenceDatasetIndicesMirrored
```
protected Vector iStoredSequenceDatasetIndicesMirrored
```
    The Vector that holds the dataset indices of stored points from a previously established list in the mirrored spectra.
  - iAnnotations
```
protected Vector iAnnotations
```
    The Vector that holds a set of Annotation instances.
  - iAnnotationsMirroredSpectra
```
protected Vector iAnnotationsMirroredSpectra
```
    The Vector that holds a set of Annotation instances for the mirrored spectra.
  - iMinDrag
```
protected int iMinDrag
```
    Minimal dragging distance in pixels.
  - iCurrentDrawStyle
```
protected GraphicsPanel.DrawingStyle iCurrentDrawStyle
```
    This variable holds the current drawing style.
  - iDotRadius
```
protected int iDotRadius
```
    This variable holds the dot radius; only used when drawing style is DOTS style.
  - iMSLevel
```
protected int iMSLevel
```
    The ms level of the current spectrum. O is assumed to mean no ms level given.
  - showAllPeaks
```
protected boolean showAllPeaks
```
    If false, only the annotated peaks will be shown. Note that this setting is ignored in profile mode!
  - yAxisZoomExcludesBackgroundPeaks
```
protected boolean yAxisZoomExcludesBackgroundPeaks
```
    If true, the automatic y-axis zoom excludes the background peaks. False includes all peaks in the zoom.
  - annotateHighestPeak
```
protected boolean annotateHighestPeak
```
    If more than one peak is within the accuracy range of an annotation setting this to true will always select the most intense of possible peaks. Setting this variable to false will instead select the most accurate peak.
  - currentGraphicsPanelType
```
protected GraphicsPanel.GraphicsPanelType currentGraphicsPanelType
```
    Sets the current GraphicsPanel type, default to centroid spectrum.
- Constructor Detail
  - GraphicsPanel
```
public GraphicsPanel()
```
- Method Detail
  - isAnnotateHighestPeak
```
public boolean isAnnotateHighestPeak()
```
    Returns true if the most intense of possible peaks to annotate is to be selected, false if the most accurate is to be selected.
    
    Returns:
    
    true if the most intense of possible peaks to annotate is to be selected, false if the most accurate is to be selected
  - setAnnotateHighestPeak
```
public void setAnnotateHighestPeak(boolean annotateHighestPeak)
```
    Set if the most intense of possible peaks to annotate is to be selected, false if the most accurate is to be selected.
    
    Parameters:
    
    annotateHighestPeak - if the most intense of possible peaks to annotate is to be selected, false if the most accurate is to be selected
  - isSubscriptAnnotationNumbers
```
public boolean isSubscriptAnnotationNumbers()
```
    Returns true if the numbers in the peak annotations are to be subscripted.
    
    Returns:
    
    true if the numbers in the peak annotations are to be subscripted
  - setSubscriptAnnotationNumbers
```
public void setSubscriptAnnotationNumbers(boolean subscriptAnnotationNumbers)
```
    Set if the numbers in the peak annotations are to be subscripted.
    
    Parameters:
    
    subscriptAnnotationNumbers - set if the numbers in the peak annotations are to be subscripted
  - yAxisZoomOnlyExcludesBackgroundPeaks
```
public boolean yAxisZoomOnlyExcludesBackgroundPeaks()
```
    Returns true if the automatic y-axis zoom excludes background peaks. False if includes all peaks.
    
    Returns:
    
    true if the automatic y-axis zoom only excludes background peaks
  - setYAxisZoomExcludesBackgroundPeaks
```
public void setYAxisZoomExcludesBackgroundPeaks(boolean yAxisZoomExcludesBackgroundPeaks)
```
    Set if the automatic y-axis zoom only considers the annotated peaks.
    
    Parameters:
    
    yAxisZoomExcludesBackgroundPeaks - if the automatic y-axis zoom only considers the annotated peaks
  - useMassDeltaCombinations
```
public boolean useMassDeltaCombinations()
```
    If true, pairs of delta mass annotations are used when doing de novo sequencing. If false, only single delta masses are annotated.
    
    Returns:
    
    the useMassDeltaCombinations if pairs of delta mass annotations are used when doing de novo sequencing
  - setUseMassDeltaCombinations
```
public void setUseMassDeltaCombinations(boolean useMassDeltaCombinations)
```
    If true, pairs of delta mass annotations are used when doing de novo sequencing. If false, only single delta masses are annotated.
    
    Parameters:
    
    useMassDeltaCombinations - the useMassDeltaCombinations to set
  - showPrecursorDetails
```
public boolean showPrecursorDetails()
```
    Returns true of the precursor details are to be shown.
    
    Returns:
    
    true of the precursor details are to be show
  - setShowPrecursorDetails
```
public void setShowPrecursorDetails(boolean showPrecursorDetails)
```
    Set whether the precursor details are to be shown.
    
    Parameters:
    
    showPrecursorDetails - the showPrecursorDetails to set
  - showResolution
```
public boolean showResolution()
```
    Returns true if the resolution is to be shown.
    
    Returns:
    
    true of the resolution is to be shown
  - setShowResolution
```
public void setShowResolution(boolean showResolution)
```
    Set whether the resolution is to be shown.
    
    Parameters:
    
    showResolution - the showResolution to set
  - yDataIsPositive
```
public boolean yDataIsPositive()
```
    Returns true of all the y-data is to be assumed as positive.
    
    Returns:
    
    true of all the y-data is to be assumed as positive
  - setYDataIsPositive
```
public void setYDataIsPositive(boolean yDataIsPositive)
```
    Set to true of all y data values can be assumed to be positive.
    
    Parameters:
    
    yDataIsPositive - true of all y data values can be assumed to be positive
  - isMiniature
```
public boolean isMiniature()
```
    Returns true if the graphics panel is to be drawn in a miniature form.
    
    Returns:
    
    true if the graphics panel is to be drawn in a miniature form
  - setMiniature
```
public void setMiniature(boolean miniature)
```
    Set if the graphics panel is to be drawn in a miniature form.
    
    Parameters:
    
    miniature - if the spectrum is to be drawn in a miniature form
  - getXAxisZoomRangeLowerValue
```
public double getXAxisZoomRangeLowerValue()
```
    Returns the lower range for the current zoom range.
    
    Returns:
    
    the lower range for the current zoom range
  - getXAxisZoomRangeUpperValue
```
public double getXAxisZoomRangeUpperValue()
```
    Returns the upper range for the current zoom range.
    
    Returns:
    
    the upper range for the current zoom range
  - getDeltaMassWindow
```
public double getDeltaMassWindow()
```
    Get the size of the window to use when searching for matches in the known masses list when the user hovers over a second data point after clicking a previous data point.
    
    Returns:
    
    the size of the delta mass window
  - setDeltaMassWindow
```
public void setDeltaMassWindow(double deltaMassWindow)
```
    Set the size of the window to use when searching for matches in the known masses list when the user hovers over a second data point after clicking a previous data point.
    
    Parameters:
    
    deltaMassWindow - the new size of the delta mass window
  - getKnownMassDeltas
```
public static HashMap<Double,String> getKnownMassDeltas()
```
    Get all the known mass deltas (if any). The keys are the Doubles with the massdelta, the values are the descriptions.
    
    Returns:
    
    HashMap of the known mass deltas
  - setKnownMassDeltas
```
public static void setKnownMassDeltas(HashMap<Double,String> aiKnownMassDeltas)
```
    Set all the known mass deltas (if any). The keys are the Doubles with the massdelta, the values are the descriptions.
    
    Parameters:
    
    aiKnownMassDeltas - the HasMap of the known mass deltas
  - getXAxisData
```
public ArrayList<double[]> getXAxisData()
```
    Returns the x-axis data.
    
    Returns:
    
    the x-axis data
  - getYAxisData
```
public ArrayList<double[]> getYAxisData()
```
    Returns the y-axis data.
    
    Returns:
    
    the y-axis data
  - getAlphaLevel
```
public float getAlphaLevel()
```
    Returns the alpha level.
    
    Returns:
    
    the alphaLevel
  - setAlphaLevel
```
public void setAlphaLevel(float alphaLevel)
```
    Sets the alpha level
    
    Parameters:
    
    alphaLevel - the alphaLevel to set
  - setXAxisStartAtZero
```
public void setXAxisStartAtZero(boolean aXAxisStartAtZero)
```
    This method sets the start value of the x-axis to zero.
    
    Parameters:
    
    aXAxisStartAtZero - if true the x axis starts at zero
  - setMaxPadding
```
public void setMaxPadding(int aMaxPadding)
```
    Set the max padding (distance between the axes and the border of the panel).
    
    Parameters:
    
    aMaxPadding - the new max padding
  - getMaxPadding
```
public int getMaxPadding()
```
    Returns the max padding (distance between the axes and the border of the panel).
    
    Returns:
    
    the max padding
  - getPeakWidth
```
public float getPeakWidth()
```
    Returns the current width of the peaks.
    
    Returns:
    
    the peak width
  - setPeakWidth
```
public void setPeakWidth(float peakWidth)
```
    Set the peak width.
    
    Parameters:
    
    peakWidth - the new peak width
  - getBackgroundPeakWidth
```
public float getBackgroundPeakWidth()
```
    Returns the current width of the background peaks.
    
    Returns:
    
    the peak width
  - setBackgroundPeakWidth
```
public void setBackgroundPeakWidth(float backgroundPeakWidth)
```
    Set the backgroundPeakWidth peak width.
    
    Parameters:
    
    backgroundPeakWidth - the new backgroundPeakWidth peak width
  - setAnnotations
```
public void setAnnotations(List<SpectrumAnnotation> aAnnotations,
                           boolean annotateHighestPeak)
```
    This method sets all the annotations on this instance. Passing a 'null' value for the Vector will result in simply removing all annotations. Do note that this method will attempt to remove duplicate annotations on a point by deleting any annotation for which the combination of annotation label and annotation x-axis value has been seen before!
    
    Parameters:
    
    aAnnotations - Vector with SpectrumAnnotation instances.
    
    annotateHighestPeak - boolean indicating if the most intense peak within the accuracy range (true) or the most accurate peak (false) is to be annotated
  - setAnnotations
```
public void setAnnotations(List<SpectrumAnnotation> aAnnotations)
```
    This method sets all the annotations on this instance. Passing a 'null' value for the Vector will result in simply removing all annotations. Do note that this method will attempt to remove duplicate annotations on a point by deleting any annotation for which the combination of annotation label and annotation x-axis value has been seen before!
    
    Parameters:
    
    aAnnotations - Vector with SpectrumAnnotation instances.
  - setAnnotationsMirrored
```
public void setAnnotationsMirrored(List<SpectrumAnnotation> aAnnotations,
                                   boolean annotateHighestPeak)
```
    This method sets all the annotations for the mirrored spectra. Passing a 'null' value for the Vector will result in simply removing all annotations. Do note that this method will attempt to remove duplicate annotations on a point by deleting any annotation for which the combination of annotation label and annotation x-axis value has been seen before!
    
    Parameters:
    
    aAnnotations - Vector with SpectrumAnnotation instances
    
    annotateHighestPeak - boolean indicating if the most intense peak within the accuracy range (true) or the most accurate peak (false) is to be annotated
  - setAnnotationsMirrored
```
public void setAnnotationsMirrored(List<SpectrumAnnotation> aAnnotations)
```
    This method sets all the annotations for the mirrored spectra. Passing a 'null' value for the Vector will result in simply removing all annotations. Do note that this method will attempt to remove duplicate annotations on a point by deleting any annotation for which the combination of annotation label and annotation x-axis value has been seen before!
    
    Parameters:
    
    aAnnotations - Vector with SpectrumAnnotation instances
  - setAnnotationYAxisThreshold
```
public void setAnnotationYAxisThreshold(double aThreshold)
```
    This method allows the caller to set the minimal non-inclusive y-axis value threshold in percent (compared to the highest point in the spectrum or chromatogram) a point must pass before being eligible for annotation.
    
    Parameters:
    
    aThreshold - double with the minimal y-axis value in percent (as compared to the highest point in the spectrum or chromatogram) cutoff threshold for annotation.
  - setFilenameColor
```
public void setFilenameColor(Color aFilenameColor)
```
    This method sets the display color for the filename on the panel. Can be 'null' for default coloring.
    
    Parameters:
    
    aFilenameColor - Color to render the filename in on the panel. Can be 'null' for default coloring.
  - getiXAxisMin
```
public double getiXAxisMin()
```
    Returns the minimum value of the x-axis.
    
    Returns:
    
    the minimum the axis value
  - setiXAxisMin
```
public void setiXAxisMin(double aXAxisMin)
```
    Sets the minimum value for the x-axis.
    
    Parameters:
    
    aXAxisMin - double with the minimum x-axis value
  - getiXAxisMax
```
public double getiXAxisMax()
```
    Returns the maximum value of the x-axis.
    
    Returns:
    
    the maximum x axis value
  - setiXAxisMax
```
public void setiXAxisMax(double aXAxisMax)
```
    Sets the maximum value for the x-axis.
    
    Parameters:
    
    aXAxisMax - double with the maximum x-axis value
  - getiYAxisMin
```
public double getiYAxisMin()
```
    Returns the minimum value of the y-axis.
    
    Returns:
    
    the minimum y axis value
  - setiYAxisMin
```
public void setiYAxisMin(double aYAxisMin)
```
    Sets the minimum value for the y-axis.
    
    Parameters:
    
    aYAxisMin - double with the minimum y-axis value
  - getiYAxisMax
```
public double getiYAxisMax()
```
    Returns the maximum value of the y-axis.
    
    Returns:
    
    the maximum y axis value
  - setiYAxisMax
```
public void setiYAxisMax(double aYAxisMax)
```
    Sets the maximum value for the y-axis.
    
    Parameters:
    
    aYAxisMax - double with the maximum y-axis value
  - paint
```
public void paint(Graphics g)
```
    Invoked by Swing to draw components. Applications should not invoke paint directly, but should instead use the repaint method to schedule the component for redrawing.
    This method actually delegates the work of painting to three protected methods: paintComponent, paintBorder, and paintChildren. They're called in the order listed to ensure that children appear on top of component itself. Generally speaking, the component and its children should not paint in the insets area allocated to the border. Subclasses can just override this method, as always. A subclass that just wants to specialize the UI (look and feel) delegate's paint method should just override paintComponent.
    
    Overrides:
    
    paint in class JComponent
    
    Parameters:
    
    g - the Graphics context in which to paint
    
    See Also:
    
    JComponent.paintComponent(java.awt.Graphics), JComponent.paintBorder(java.awt.Graphics), JComponent.paintChildren(java.awt.Graphics), JComponent.getComponentGraphics(java.awt.Graphics), JComponent.repaint(long, int, int, int, int)
  - annotatePeaks
```
protected void annotatePeaks(Graphics g,
                             Vector annotations,
                             boolean mirrored)
```
    Annotate the annotated peaks.
    
    Parameters:
    
    g - the Graphics context in which to paint
    
    annotations - the annotations
    
    mirrored - if the annotations are for the mirrored spectra
  - drawDaisyChain
```
protected void drawDaisyChain(Graphics g,
                              Vector clickedList,
                              Vector clickedListDatasetIndices,
                              int clickedIndex,
                              int clickedDataSetIndex,
                              Vector storedSequence,
                              Vector storedSequenceDatasetIndices,
                              boolean mirrored)
```
    Draw daisy chains.
    
    Parameters:
    
    g - the Graphics context in which to paint
    
    clickedList - vector that holds all points clicked up to now
    
    clickedListDatasetIndices - vector that holds the dataset indices of all points clicked up to now
    
    clickedIndex - int that indicates which point was clicked
    
    clickedDataSetIndex - int that indicates which dataset contains the clicked point
    
    storedSequence - vector that holds a set of stored points from a previously established list
    
    storedSequenceDatasetIndices - vector that holds the dataset indices of stored points from a previously established list.
    
    mirrored - if the daisy chains are for the mirrored spectra
  - drawXAxisReferenceAreas
```
protected void drawXAxisReferenceAreas(Graphics g,
                                       boolean drawOnTop)
```
    Draws the x-axis reference areas if any.
    
    Parameters:
    
    g - Graphics object to draw on.
    
    drawOnTop - if true the areas to be drawn on top of the data are drawn, if false the areas that are to be drawn behind the data are drawn
  - drawYAxisReferenceAreas
```
protected void drawYAxisReferenceAreas(Graphics g,
                                       boolean drawOnTop)
```
    Draws the y-axis reference areas if any.
    
    Parameters:
    
    g - Graphics object to draw on.
    
    drawOnTop - if true the areas to be drawn on top of the data are drawn, if false the areas that are to be drawn behind the data are drawn
  - getMaxXAxisValue
```
public double getMaxXAxisValue()
```
    This method reports on the largest x-axis value in the point collection across all datasets.
    
    Returns:
    
    double with the largest x-axis value in the point collection.
  - getMinXAxisValue
```
public double getMinXAxisValue()
```
    This method reports on the smallest x-axis value in the point collection across all datasets.
    
    Returns:
    
    double with the smallest x-axis value in the point collection.
  - addSpectrumPanelListener
```
public void addSpectrumPanelListener(SpectrumPanelListener aListener)
```
    This method registers the specified SpectrumPanelListener with this instance and notifies it of all future events. The Listeners will be notified in order of addition (first addition is notified first).
    
    Parameters:
    
    aListener - SpectrumPanelListener to register on this instance.
  - addListeners
```
protected void addListeners()
```
    This method adds the event listeners to the panel.
  - rescale
```
public void rescale(double aMinXAxisValue,
                    double aMaxXAxisValue)
```
    This method rescales the x-axis while notifying the observers.
    
    Parameters:
    
    aMinXAxisValue - double with the new minimum x-axis value to display.
    
    aMaxXAxisValue - double with the new maximum x-axis value to display.
  - addReferenceAreaXAxis
```
public void addReferenceAreaXAxis(ReferenceArea referenceArea)
```
    Add a x-axis reference area.
    
    Parameters:
    
    referenceArea - the reference area to add
  - removeReferenceAreaXAxis
```
public void removeReferenceAreaXAxis(String identifier)
```
    Removes the x-axis reference area with the given identifier. Does nothing if no reference with the given identifier is found.
    
    Parameters:
    
    identifier - the identifier of the reference to remove
  - removeAllReferenceAreasXAxis
```
public void removeAllReferenceAreasXAxis()
```
    Removes all the x-axis reference areas.
  - getAllReferenceAreasXAxis
```
public HashMap<String,ReferenceArea> getAllReferenceAreasXAxis()
```
    Returns all the x-axis references areas as a hashmap, with the labels as the keys.
    
    Returns:
    
    hashmap of all reference areas
  - addReferenceAreaYAxis
```
public void addReferenceAreaYAxis(ReferenceArea referenceArea)
```
    Add a y-axis reference area.
    
    Parameters:
    
    referenceArea - the reference area to add
  - removeReferenceAreaYAxis
```
public void removeReferenceAreaYAxis(String identifier)
```
    Removes the y-axis reference area with the given identifier. Does nothing if no reference with the given identifier is found.
    
    Parameters:
    
    identifier - the identifier of the reference to remove
  - removeAllReferenceAreasYAxis
```
public void removeAllReferenceAreasYAxis()
```
    Removes all the y-axis reference areas.
  - getAllReferenceAreasYAxis
```
public HashMap<String,ReferenceArea> getAllReferenceAreasYAxis()
```
    Returns all the y-axis references areas as a hashmap, with the labels as the keys.
    
    Returns:
    
    hashmap of all reference areas
  - setDataPointAndLineColor
```
public void setDataPointAndLineColor(Color aColor,
                                     int index)
```
    Sets the color of data points and line for the dataset with the given dataset index. Index starts at 0.
    
    Parameters:
    
    aColor - the color to use
    
    index - the index of the dataset
  - setAreaUnderCurveColor
```
public void setAreaUnderCurveColor(Color aColor,
                                   int index)
```
    Sets the color of the area under the curve for profile chromatograms and spectra for the dataset with the given dataset index. Index starts at 0.
    
    Parameters:
    
    aColor - the color to use
    
    index - the index of the dataset
  - getAreaUnderCurveColors
```
public ArrayList<Color> getAreaUnderCurveColors()
```
    Returns the list of colors used for the datasets. Index on dataset. Index starts at 0.
    
    Returns:
    
    the the list of colors used for the datasets
  - rescale
```
public void rescale(double aMinXAxisValue,
                    double aMaxXAxisValue,
                    boolean aNotifyListeners)
```
    This method rescales the x-axis, allowing the caller to specify whether the observers need be notified.
    
    Parameters:
    
    aMinXAxisValue - double with the new minimum x-axis value to display.
    
    aMaxXAxisValue - double with the new maximum x-axis value to display.
    
    aNotifyListeners - boolean to indicate whether the observers should be notified.
  - processXAndYData
```
protected void processXAndYData(double[] aXAxisData,
                                double[] aYAxisData,
                                Color dataPointAndLineColor,
                                Color areaUnderCurveColor)
```
    This method reads the x and y values from the specified arrays and stores these internally for drawing. The x-axis values are sorted in this step.
    
    Parameters:
    
    aXAxisData - double[] with the x-axis values.
    
    aYAxisData - double[] with the corresponding y-axis values.
    
    dataPointAndLineColor - the color to use for the data points and line
    
    areaUnderCurveColor - the color to use for the area under the curve
  - processMirroredXAndYData
```
protected void processMirroredXAndYData(double[] aXAxisData,
                                        double[] aYAxisData,
                                        Color dataPointAndLineColor,
                                        Color areaUnderCurveColor)
```
    This method reads the x and y values from the specified arrays and stores these internally for drawing. The x-axis values are sorted in this step.
    
    Parameters:
    
    aXAxisData - double[] with the x-axis values.
    
    aYAxisData - double[] with the corresponding y-axis values.
    
    dataPointAndLineColor - the color to use for the data points and line
    
    areaUnderCurveColor - the color to use for the area under the curve
  - drawAxes
```
protected int[] drawAxes(Graphics g,
                         double aXMin,
                         double aXMax,
                         int aXScale,
                         double aYMin,
                         double aYMax)
```
    This method draws the axes and their labels on the specified Graphics object, taking into account the padding.
    
    Parameters:
    
    g - Graphics object to draw on.
    
    aXMin - double with the minimal x value.
    
    aXMax - double with the maximum x value.
    
    aXScale - int with the scale to display for the X-axis labels (as used in BigDecimal's setScale).
    
    aYMin - double with the minimal y value.
    
    aYMax - double with the maximum y value.
    
    Returns:
    
    int[] with the length of the X axis and Y axis respectively.
  - drawXTags
```
protected void drawXTags(Graphics g,
                         int aMin,
                         int aMax,
                         int aXScale,
                         int aXAxisWidth,
                         int aPadding)
```
    This method draws tags on the X axis.
    
    Parameters:
    
    aMin - double with the minimum value for the axis.
    
    aMax - double with the maximum value for the axis.
    
    aXScale - int with the scale to display for the X-axis labels (as used in BigDecimal's setScale).
    
    g - Graphics object to draw on.
    
    aXAxisWidth - int with the axis width in pixels.
    
    aPadding - int with the amount of padding to take into account.
  - drawYTags
```
protected void drawYTags(Graphics g,
                         int aMin,
                         int aMax,
                         int aYAxisHeight,
                         int aPadding)
```
    This method draws tags on the Y axis.
    
    Parameters:
    
    aMin - double with the minimum value for the axis.
    
    aMax - double with the maximum value for the axis.
    
    g - Graphics object to draw on.
    
    aYAxisHeight - int with the axis height in pixels.
    
    aPadding - int with the amount of padding to take into account.
  - highLightPeak
```
protected void highLightPeak(int aIndex,
                             int dataSetIndex,
                             Graphics g,
                             boolean mirrored)
```
    This method will draw a highlighting triangle + x-value on top of the marked point.
    
    Parameters:
    
    aIndex - int with the index of the point to highlight
    
    dataSetIndex - the index of the dataset
    
    g - Graphics object to draw the highlighting on
    
    mirrored - if true the highlighted peak is from a mirrored spectrum
  - highlightClicked
```
protected void highlightClicked(int aIndex,
                                int dataSetIndex,
                                Graphics g,
                                boolean mirrored)
```
    This method will draw a highlighting triangle + x-value on top of the clicked marked point.
    
    Parameters:
    
    aIndex - int with the index of the clicked point to highlight
    
    dataSetIndex - the index of the dataset
    
    g - Graphics object to draw the highlighting on
    
    mirrored - if true the highlighted peak is from a mirrored spectrum
  - highLight
```
protected void highLight(int aIndex,
                         int dataSetIndex,
                         Graphics g,
                         Color aColor,
                         String aComment,
                         int aPixelsSpacer,
                         boolean aShowArrow,
                         int aAnnotationCounter,
                         boolean mirrored)
```
    This method will highlight the specified point in the specified color by drawing a floating triangle + x-value above it.
    
    Parameters:
    
    aIndex - int with the index.
    
    dataSetIndex - the index of the dataset
    
    g - Graphics object to draw on
    
    aColor - Color to draw the highlighting in.
    
    aComment - String with an optional comment. Can be 'null' in which case it will be omitted.
    
    aPixelsSpacer - int that gives the vertical spacer in pixels for the highlighting.
    
    aShowArrow - boolean that indicates whether a downward-pointing arrow and dotted line should be drawn over the point.
    
    aAnnotationCounter - the number of annotation of the given peak
    
    mirrored - if true the highlighting is done on the mirrored spectra
  - drawMeasurementLine
```
protected void drawMeasurementLine(int aFirstIndex,
                                   int aFirstDatasetIndex,
                                   int aSecondIndex,
                                   int aSecondDatasetIndex,
                                   Graphics g,
                                   Color aColor,
                                   int aExtraPadding,
                                   boolean mirrored)
```
    This method draws a line, measuring the distance between two points in real mass units.
    
    Parameters:
    
    aFirstIndex - int with the first point index to draw from.
    
    aFirstDatasetIndex - the dataset index of the first data point
    
    aSecondIndex - int with the second point index to draw to.
    
    aSecondDatasetIndex - the dataset index of the second data point
    
    g - Graphics object on which to draw.
    
    aColor - Color object with the color for all the drawing.
    
    aExtraPadding - int with an optional amount of extra padding (lower on the graph if positive, higher on the graph if negative)
    
    mirrored - if true the line is drawn for the mirrored spectra
  - dropDottedLine
```
protected void dropDottedLine(int aPeakIndex,
                              int aDatasetIndex,
                              int aTotalHeight,
                              Graphics g,
                              boolean mirrored)
```
    This method drops a dotted line from the specified total height to the top of the indicated point.
    
    Parameters:
    
    aPeakIndex - int with the index of the point to draw the dotted line for.
    
    aDatasetIndex - the index of the dataset
    
    aTotalHeight - int with the height (in pixels) to drop the dotted line from.
    
    g - Graphics object to draw the dotted line on.
    
    mirrored - if true the line is drawn on the mirrored spectra
  - findDeltaMassMatches
```
protected String findDeltaMassMatches(double aDelta,
                                      double aWindow)
```
    This method attempts to find a list of known mass deltas, corresponding with the specified x value in the given window.
    
    Parameters:
    
    aDelta - the delta mass to search for
    
    aWindow - the window used for the search
    
    Returns:
    
    String with the description of the matching mass delta or empty String if none was found.
  - annotate
```
protected void annotate(SpectrumAnnotation aSA,
                        Graphics g,
                        HashMap<String,Integer> aAlreadyAnnotated,
                        boolean mirrored)
```
    This method attempts to find the specified SpectrumAnnotation in the current peak list and if so, annotates it correspondingly on the screen.
    
    Parameters:
    
    aSA - SpectrumAnnotation with the annotation to find.
    
    g - Graphics instance to annotate on.
    
    aAlreadyAnnotated - HashMap with the index of a point as key, and the number of times it has been annotated as value (or 'null' if not yet annotated).
    
    mirrored - if true the annotation is for the mirrored spectra
  - drawMirroredPeaks
```
protected void drawMirroredPeaks(Graphics g)
```
    This method draws all of the peaks for all datasets in the current x-axis range on the panel.
    
    Parameters:
    
    g - Graphics object to draw on.
  - drawPeaks
```
protected void drawPeaks(Graphics g)
```
    This method draws all of the peaks for all datasets in the current x-axis range on the panel.
    
    Parameters:
    
    g - Graphics object to draw on.
  - drawFilledPolygon
```
protected void drawFilledPolygon(Graphics g)
```
    This method draws filled polygons for all of the peaks for all datasets in the current x-axis range on the panel.
    
    Parameters:
    
    g - Graphics object to draw on.
  - setScientificXAxis
```
public void setScientificXAxis(boolean scientificXAxis)
```
    Set if the x-axis tags are to be drawn using scientific annotation. The default is false. The default pattern is "##0.#####E0".
    
    Parameters:
    
    scientificXAxis - if the x-axis tags is to be drawn using scientific annotation
  - setScientificXAxis
```
public void setScientificXAxis(String pattern)
```
    Set if the x-axis tags are to be drawn using scientific annotation. The default is false. For pattern details see java.text.DecimalFormat. The default pattern is "##0.#####E0".
    
    Parameters:
    
    pattern - the number format pattern to use
  - setScientificYAxis
```
public void setScientificYAxis(boolean scientificYAxis)
```
    Set if the y-axis tags are to be drawn using scientific annotation. The default is false. The default pattern is "##0.#####E0".
    
    Parameters:
    
    scientificYAxis - if the y-axis tags is to be drawn using scientific annotation
  - setScientificYAxis
```
public void setScientificYAxis(String pattern)
```
    Set if the y-axis tags are to be drawn using scientific annotation. The default is false. For pattern details see java.text.DecimalFormat. The default pattern is "##0.#####E0".
    
    Parameters:
    
    pattern - the number format pattern to use
  - getPeakWaterMarkColor
```
public Color getPeakWaterMarkColor()
```
    Get the peak water mark color.
    
    Returns:
    
    the peak water mark color
  - setPeakWaterMarkColor
```
public void setPeakWaterMarkColor(Color peakWaterMarkColor)
```
    Set the peak water mark color.
    
    Parameters:
    
    peakWaterMarkColor - the color to set

Class GraphicsPanel

Nested Class Summary

Nested classes/interfaces inherited from class javax.swing.JPanel

Nested classes/interfaces inherited from class javax.swing.JComponent

Nested classes/interfaces inherited from class java.awt.Container

Nested classes/interfaces inherited from class java.awt.Component

Field Summary

Fields inherited from class javax.swing.JComponent

Fields inherited from class java.awt.Component

Fields inherited from interface java.awt.image.ImageObserver

Constructor Summary

Method Summary

Methods inherited from class javax.swing.JPanel

Methods inherited from class javax.swing.JComponent

Methods inherited from class java.awt.Container

Methods inherited from class java.awt.Component

Methods inherited from class java.lang.Object

Field Detail

miniature

yDataIsPositive

alphaLevel

dataSetCounter

dataSetCounterMirroredSpectra

INTERACTIVE_STATUS

ANNOTATED_STATUS

iKnownMassDeltas

deltaMassWindow

iXAxisLabel

iYAxisLabel

iFilenameColor

iDataPointAndLineColor

iDataPointAndLineColorMirroredSpectra

iAreaUnderCurveColor

iAreaUnderCurveColorMirroredSpectra

iPointSize

iFilename

iFilenameMirrorredSpectrum

iSpecPanelListeners

iPointDetectionTolerance

iStartXLoc

iStartYLoc

iEndXLoc

xAxisZoomRangeLowerValue

xAxisZoomRangeUpperValue

iDragXLoc

iXScaleUnit

iYScaleUnit

iXUnit

iYUnit

iXPadding

iTopPadding

iXAxisStartAtZero

iDragged

xTagCount

yTagCount

padding

currentPadding

maxPadding

showFileName

showPrecursorDetails

showResolution

iXAxisData

iXAxisDataMirroredSpectrum

iXAxisMin

iXAxisMax

iYAxisMin

iYAxisMax

iAnnotationYAxisThreshold

iYAxisData

iYAxisDataMirroredSpectrum

iPrecursorMZ

iPrecursorMZMirroredSpectrum

iPrecursorCharge

iPrecursorChargeMirorredSpectrum

iXAxisDataInPixels

iYAxisDataInPixels

iXAxisDataInPixelsMirroredSpectrum

iYAxisDataInPixelsMirroredSpectrum

iHighLight

iHighLightMirrored